iTunes is already something of a bloated mess. They really need a central iCloud app that handles all syncing, including iOS devices. Then pare down iTunes and let it focus on what made it great in the first place: organizing music. I'd also break out video playback into a separate app. It already is on iPads, which makes it even more confusing for people, having different places to find the same stuff on different devices....and don't forget iPhoto (for some odd reason) imports videos too. It's a mess. Every type of media or data should have its own app, and its own store (all linked to your Apple ID, of course).
iCloud - oversees syncing everything, managing devices, lets you select in one interface what media you want to sync, and to where.
- App Store - apps, and maybe include managing home screen icons here.
- iTunes - music, and only music (OK, audio, including podcasts), includes iTunes Store for audio content.
- Video - videos (for playback), includes video store for video content.
- iPhoto - photos
- iBook - books, includes iBooks Store
- Others - handle their own data: iCal, Address Book